[gmx-users] N-glycosylation of a protein

[Steffen Wolf]

Hi Eric,
one way to fix the problem is to define a residue in the force field
.rtp file for a "new" amino acid consisting of Asn + the hydrocarbon.
That way GROMACS can create the topology of the holoprotein while
running pdb2gmx over it.
Hope that helps
Steffen
> Hi,
> I try to start a simulation with a N-glycosylated protein. I used
> glyprot to attach the sugar chains to the asn residues. But then.. I
> create a topology for the sugars, then merge it with the toplogy of
> the protein? What about the linkage between the protein and the sugar?
>
> Thanks,
> Eric
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
Dipl.-Chem. Steffen Wolf
Fellow of the Ruhr-University Research School
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: swolf at bph.rub.de
Web: http://www.bph.rub.de